fixing pint redifinition warnings

Author: matthiaskoenig

src/sbmlsim/combine/sedml/parser.py

@@ -866,7 +866,7 @@ def __init__(
         self.name: str = name
 
         # unit registry to handle units throughout the simulation
-        self.ureg: UnitRegistry = UnitRegistry()
+        self.ureg: UnitRegistry = UnitRegistry(on_redefinition='ignore')
 
         # Reference to the experiment class
         self.exp_class: Type[SimulationExperiment]

src/sbmlsim/simulation/scan.py

@@ -144,7 +144,7 @@ def to_simulations(self):
     from sbmlsim.simulation import Timecourse, TimecourseSim
     from sbmlsim.units import UnitRegistry
 
-    ureg = UnitRegistry()
+    ureg = UnitRegistry(on_redefinition='ignore')
     Q_ = ureg.Quantity
     uinfo = UnitsInformation(
         udict={k: "dimensionless" for k in ["X", "[X]", "n", "Y"]}, ureg=ureg

src/sbmlsim/test/test_data.py

@@ -8,15 +8,15 @@
 
 def test_dataset():
     df = pd.DataFrame({"col1": [1, 2, 3], "col2": [2, 3, 4], "col3": [4, 5, 6]})
-    dset = DataSet.from_df(df, udict={"col1": "mM"}, ureg=UnitRegistry())
+    dset = DataSet.from_df(df, udict={"col1": "mM"}, ureg=UnitRegistry(on_redefinition='ignore'))
     assert "col1" in dset.uinfo
     assert dset.uinfo["col1"] == "mM"
 
 
 def test_Faber1978_Fig1():
     data_path = DATA_DIR / "datasets"
     df = load_pkdb_dataframe(sid="Faber1978_Fig1", data_path=data_path)
-    dset = DataSet.from_df(df, udict={}, ureg=UnitRegistry())
+    dset = DataSet.from_df(df, udict={}, ureg=UnitRegistry(on_redefinition='ignore'))
     assert "cpep" in dset.uinfo
     assert "time" in dset.uinfo
     assert dset.uinfo["time"] == "min"
@@ -31,7 +31,7 @@ def test_Allonen1981_Fig3A():
     data_path = DATA_DIR / "datasets"
     df = load_pkdb_dataframe(sid="Allonen1981_Fig3A", data_path=data_path)
     for substance in df.substance.unique():
-        dset = DataSet.from_df(df[df.substance == substance], ureg=UnitRegistry())
+        dset = DataSet.from_df(df[df.substance == substance], ureg=UnitRegistry(on_redefinition='ignore'))
 
         assert "mean" in dset.uinfo
         assert "time" in dset.uinfo
@@ -48,7 +48,7 @@ def test_unit_conversion1():
     data_path = DATA_DIR / "datasets"
     df = load_pkdb_dataframe(sid="Allonen1981_Fig3A", data_path=data_path)
 
-    ureg = UnitRegistry()
+    ureg = UnitRegistry(on_redefinition='ignore')
     Q_ = ureg.Quantity
     Mr = Q_(300, "g/mole")
     for substance in df.substance.unique():

src/sbmlsim/units.py

@@ -284,7 +284,7 @@ def from_sbml_doc(
     @staticmethod
     def _default_ureg() -> pint.UnitRegistry:
         """Get default unit registry."""
-        ureg = pint.UnitRegistry()
+        ureg = pint.UnitRegistry(on_redefinition='ignore')
         ureg.define("none = count")
         ureg.define("item = count")
         ureg.define("percent = 0.01*count")
@@ -445,6 +445,6 @@ def udef_to_str(cls, udef: libsbml.UnitDefinition) -> str:
     from sbmlsim.test import MODEL_DEMO, MODEL_GLCWB
 
     model_path = MODEL_DEMO
-    ureg = UnitRegistry()
+    ureg = UnitRegistry(on_redefinition='ignore')
     uinfo = UnitsInformation.from_sbml(model_path, ureg=ureg)
     console.log(uinfo.udict)